JAL-2759 Minor doc and naming changes

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 93791e4..18afa5b 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -42,7 +42,8 @@ import java.util.concurrent.locks.ReentrantReadWriteLock;
  * 
  * - getVisibleColsIterator: iterates over the visible *columns*
  * 
- * For performance reasons, provide bounds where possible.
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
  * 
  * @author kmourao
  *
@@ -68,7 +69,7 @@ public class HiddenColumns
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private ArrayList<int[]> hiddenColumns;
+  private List<int[]> hiddenColumns;
 
   /**
    * Constructor
@@ -483,14 +484,14 @@ public class HiddenColumns
       markHiddenRegions(hidden);
       hidden.andNot(gaps);
       hiddenColumns = null;
-      this.hideMarkedBits(hidden);
+      this.hideColumns(hidden);
 
       // for each sequence in the alignment, except the profile sequence,
       // insert gaps corresponding to each hidden region but where each hidden
       // column region is shifted backwards by the number of preceding visible
       // gaps update hidden columns at the same time
       Iterator<int[]> regions = hiddenColumns.iterator();
-      ArrayList<int[]> newhidden = new ArrayList<>();
+      List<int[]> newhidden = new ArrayList<>();
 
       int numGapsBefore = 0;
       int gapPosition = 0;
@@ -1277,7 +1278,7 @@ public class HiddenColumns
    * @param inserts
    *          - columns map to bits starting from zero
    */
-  public void hideMarkedBits(BitSet inserts)
+  public void hideColumns(BitSet inserts)
   {
     try
     {
@@ -1384,7 +1385,8 @@ public class HiddenColumns
    * 
    * @param res
    *          visible residue position, unadjusted for hidden columns
-   * @return region as [start,end] or null if no matching region is found
+   * @return region as [start,end] or null if no matching region is found. If
+   *         res is adjacent to two regions, returns the left region.
    */
   public int[] getRegionWithEdgeAtRes(int res)
   {

diff --git a/src/jalview/datamodel/RegionsIterator.java b/src/jalview/datamodel/RegionsIterator.java
deleted file mode 100644 (file)
index 7eb5ff8..0000000
--- a/src/jalview/datamodel/RegionsIterator.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package jalview.datamodel;
-
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * A local iterator which iterates over hidden column regions in a range.
- * Intended for use ONLY within the HiddenColumns class, because it works
- * directly with the hiddenColumns collection without locking (callers should
- * lock hiddenColumns).
- */
-public class RegionsIterator implements Iterator<int[]>
-{
-  // start position to iterate from
-  private int start;
-
-  // end position to iterate to
-  private int end;
-
-  // current index in hiddenColumns
-  private int currentPosition = 0;
-
-  // current column in hiddenColumns
-  private int[] nextRegion = null;
-
-  private int[] currentRegion = null;
-
-  private int removedIndex = -1;
-
-  private final List<int[]> hiddenColumns;
-
-  // Constructor with bounds
-  RegionsIterator(int lowerBound, int upperBound, List<int[]> hiddenCols,
-          HiddenColumnsCursor cursor)
-  {
-    start = lowerBound;
-    end = upperBound;
-    hiddenColumns = hiddenCols;
-
-    if (hiddenColumns != null)
-    {
-      // TODO remove whole class?
-      // commented out to compile
-      // currentPosition = cursor.findRegionForColumn(start);
-
-      if (currentPosition < hiddenColumns.size())
-      {
-        nextRegion = hiddenColumns.get(currentPosition);
-      }
-    }
-  }
-
-  @Override
-  public boolean hasNext()
-  {
-    return (hiddenColumns != null) && (nextRegion != null)
-            && (nextRegion[0] <= end);
-  }
-
-  @Override
-  public int[] next()
-  {
-    currentRegion = nextRegion;
-    currentPosition++;
-    if (currentPosition < hiddenColumns.size())
-    {
-      nextRegion = hiddenColumns.get(currentPosition);
-    }
-    else
-    {
-      nextRegion = null;
-    }
-    return currentRegion;
-  }
-
-  @Override
-  public void remove()
-  {
-    if ((currentRegion != null) && (removedIndex != currentPosition))
-    {
-      currentPosition--;
-      hiddenColumns.subList(currentPosition, currentPosition + 1).clear();
-      removedIndex = currentPosition;
-    }
-    else
-    {
-      // already removed element last returned by next()
-      // or next() has not yet been called
-      throw new IllegalStateException();
-    }
-  }
-
-}

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 850a09a..1e4116d 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1503,7 +1503,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     inserts.or(mask);
 
     // and set hidden columns accordingly
-    hidden.hideMarkedBits(inserts);
+    hidden.hideColumns(inserts);
 
     ap.av.getAlignment().setHiddenColumns(hidden);
     refresh();

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 133f06e..ba2c1ea 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -689,23 +689,23 @@ public class HiddenColumnsTest
     // one hidden range
     one.set(1);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
     assertEquals(1, cs.getNumberOfRegions());
 
     one.set(2);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
     assertEquals(1, cs.getNumberOfRegions());
 
     one.set(3);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
     assertEquals(1, cs.getNumberOfRegions());
 
     // split
     one.clear(2);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
     assertEquals(2, cs.getNumberOfRegions());
 
     assertEquals(0, cs.visibleToAbsoluteColumn(0));
@@ -715,7 +715,7 @@ public class HiddenColumnsTest
     // one again
     one.clear(1);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
 
     assertEquals(1, cs.getNumberOfRegions());
 
@@ -746,7 +746,7 @@ public class HiddenColumnsTest
         assertTrue(fromMark.isEmpty());
       }
 
-      hc.hideMarkedBits(toMark);
+      hc.hideColumns(toMark);
 
       // see if we can recover bitfield
       hc.markHiddenRegions(fromMark = new BitSet());
@@ -771,7 +771,7 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = "Functional")
-  public void testGetVisibleStartAndEndIndexTest()
+  public void testGetVisibleStartAndEndIndex()
   {
     Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
     AlignmentI align = new Alignment(new SequenceI[] { seq });
@@ -1156,14 +1156,14 @@ public class HiddenColumnsTest
     HiddenColumns h2 = new HiddenColumns();
 
     BitSet tohide = new BitSet(21);
-    h.hideMarkedBits(tohide);
+    h.hideColumns(tohide);
     assertTrue(h.equals(h2));
 
     // NB in hideMarkedBits, the last bit is not set to hidden
     tohide.set(3, 6);
     tohide.set(9);
     tohide.set(19, 21);
-    h.hideMarkedBits(tohide);
+    h.hideColumns(tohide);
 
     h2.hideColumns(3, 5);
     h2.hideColumns(9, 9);